So i discovered two things, the first thing is the game save then you reached 42 Zyphoids and not then you kill a boss.
With reaching 42 Zyphoids it looks like every Zyphoid on the Worldmap despawns.
I checked two locations there i definitly not killed the Zyphoid, one was in the ship and the other in the near of the missile weapon.
it is possible to get the second Zyphoid on head near the Four Missle Upgrade, then its possible to skip the boss. Also it is possible to get 43 Zyphoids before you Enter the dungeon and need only to kill one. I need to time it, but it could be a faster route(not faster, at the moment).
Another Edit:
if you not take the Savepoint in the Ship, after the Missiles you can get one Zyphoid in the near, kill you, start in the Opening again, kill the Zyphoid and you have already three Zyphoids. But since you must play the Intro again ect. i think its not worth it
Just a random fact, you also can kill 5 Zyphoids on the map, get killed, respawn in the Opening and you have after that 7 Zyhpoids killed, two in the Opening and 5 on the map.
Edit: Edit 2: both routes should work, i tested it, so its possible to skip Kraid, without change the route and without the softlock and second Zyphoid in the dungeon. The second Zyphoid falls trough the map or so and you can actually kill it before Boss room.
I forget something, iam not sure it could work, but if you go the actual route, you can trigger the second zyphoid in kraid dungeon, kill the third one, try to get second one on you head before boss room, take the missiles, go out of Room, let Zyphoid from you head, kill it and do the warp.
Alternative you trigger second Zyphoid, go to Bossroom and do the same as before, then go to third Zyphoid and kill it and then do the warp.
